Secrets
by The Epic Writers of Fanfiction
Summary: The Doctor's adopted daughter has been travelling with the Doctor all her life. But he has never taken her to Earth. But a trip to Earth leads to so many secrets that the Doctor has hidden from her. And who is the strange boy who is trying to kill her?    ADOPTED BY TORCHWOODER98!
1. Chapter 1

With a final shake the TARDIS landed. A new place, but where? wondered the Doctor. He poked his head out. It was cold, that was for certain. He stepped outside. "Earth" he said to himself.

"2011?" he found an abandoned newspaper. It read: 'January 1st, 1951'. 'Ahh, 1951' he thought, 'the invention of the Aerocar, the car build with a freeway.' It had seemed like a good idea to him. 'I wonder why it never caught on...'

"Sir?" A young boy walked up to him. He was dressed very poorly and looked like he hadn't had a decent meal in a year. "Excuse me sir?"

'England' thought the Doctor.

"Sir could you please tell me were I can find the orphanage?"

"Umm..." replied the Doctor. He looked into the basket the boy was holding and saw two babies.

"Why do you need to take them to the orphanage?"

"We don't have the money to fill 5 people sir." The doctor looked at the basket again.

"Why don't i take them for you... Do they have names?" he asked the boy.

"Yes sir." he pointed to the girl. "That's Annie and," he pointed to the boy "that's Arthur" the boy handed him the basket and said a small good bye to Annie and Arthur who he now noticed were asleep.

"Umm, boy, how old are they?" he asked.

"Almost 12 months sir. They're birthday is next month. The 6th" the boy said. "Thank you sir."

The boy turned and ran off home without another word. The Doctor looked down at the two babies. The boy had flaming ginger hair. The girl had gently soft, honey brown curls. He looked at them a moment longer then went into the TARDIS.

"What am I to do with the two of you?" the Doctor said to himself. "Where's a woman when you need her?" He sighed and the little girl, Annie, giggled.  
>He smiled.<p>

"Aren't you cute" he said tickling her under her chin. "So Annie, where would you like to go?" She looked thoughtful before she replied.

"Goo-goo, gaga?" she said.

"No, I'm sorry, I can't take you to your mummy.." he said sadly.

"Doo-da?" she said.

"Umm... I don't know how to tell you this," he said more to himself than to her. "Well lets give it a go." He looked at her and said "Annie, sweet Annie... Mummy's... gone... away... for awhile..." He struggled with what to say, for there was no way to say that your mummy didn't want you nicely.

"' 'Ou dada?" She asked.

"Umm, sure. I'll be daddy.." He said thankful for the slight change of subject.

"Foo bo mama.." she said.

"Yes, but I'm not mummy."

Arthur coughed.

…

The Doctor stepped out, basket in hand. "Ahh! Here we are! I love this planet, it has the greatest and funniest name. Ahh but its brilliant." He looked down at Annie and Arthur who had curious looks on their faces. "Bob." He said simply with a smile. "The planet Bob! Named as a joke by astronomers who were drunk. They didn't think it was a real planet but the next night they looked and what do you know! There was Bob, still there in the sky." Annie giggled, Arthur appeared to roll his eyes. "You know, this planet takes a great respect to babies and has the biggest baby store you could ever see, maybe we should get you set up."

The Doctor carried the basket in his left hand, carefully trying not to swing it. The last time he had visited Bob, the store was full of other types of items to carry babies in. To be honest, he was getting tired of carrying them around in an old basket.

When he stepped into the store, the first place he headed to were the would be a relief to push a carriage instead of carry a basket, but still, it seemed like too much to lug around. He decided to think on that and instead headed to clothing.

The twins were only wrapped in, at the most, two blankets. The least he could do was provide the children with decent clothing.

It wasn't that he liked doing any of this, in fact, he could hardly stand breathing the air in that store, let alone actually shopping. But there was no where else to go. Besides, maybe a kindly person would see him there and take in the kids. Probably not, but it was worth a shot.

The Doctor somehow wound up in the boys clothing aisle. He looked around. Something didn't feel right. It was as if someone or something were breathing down his neck. Yet, when he looked behind him, he saw nothing. Yes, something was definitely wrong. Even Annie and Arthur looked worried, and they were only babies!

He decided to let it be for now, even though he would still be on his guard. The Doctor continued down the aisle, looking at the boy's clothing. He judged the size clothing that Arthur probably wore and picked up a few things quickly, not really paying attention to the design. Then he headed to the girl's clothing aisle.

He could still feel the eerie presence following him like a shadow. Its steps were light and silent, and he almost wondered if it was the Vashta Nerada. But he would still be able to sense the Vashta Nerada, and besides, there weren't lights burning out behind him and there were no actual shadows behind him.

He glanced at little Annie, trying to judge what size of clothing she would probably wear. But somehow, he couldn't pull his eyes away as quickly as he had with Arthur. There was a small glint in her eyes that he hadn't seen with the boy. When the Doctor looked at the boy, he felt like he was looking at an old friend, but when he looked at Annie, he felt that he could see someone else in her.

It had been so long ago, he almost didn't want to remember it, but yet the memories flooded back; the memories were of Gallifrey and what he had left behind on that lonely planet. The Doctor could already tell that Annie was so full of life and curiosity. She had enough curiosity to see the whole universe. She was almost like her...

Well, there had been so many, but the Doctor was thinking back to the first woman who had ever travelled with him. Both she and Annie shared that same glint in their eyes.

But he already knew that Annie was not her. She was disguised as a different human. He had already met with her, travelled with her, and fell in love with her all over again. There was never any way to get her back, and now he would never get the chance to tell her.

He shook his head and looked back at the clothes. He knew he had to get clothes for Annie.

He strolled through the aisle, uncomfortably aware of the presence. To anyone else, this presence may have seemed like a figment of their imagination or a result of over anxiety, but to him, he knew that something was there. He racked his brain, trying to figure out what type of species it could be, and from what planet it could be from.

He reached a section of the aisle where most of the clothes would fit Annie, and acting as though everything were normal, he looked at a few of the outfits and put them in the cart. He calmly strolled to the front desk, and stepped on.

The Doctor always hated shopping and this was one of the reasons: He never liked having to stand there and pay for whatever it was he bought. No matter what planet it was, what century it was, or what race it was, he never got any customer service. He always got a funny look when he tried to explain that he couldn't exactly pay; that the fate of the universe rested in his hands and he had no time to stand there and wait for his change.

However, there were times like this where there wasn't anyone at the desk. Actually, there wasn't really a desk. It was more like an ATM on earth. The "cashier" was actually a computer.

Thankfully, he actually did have the currency for this planet with him. He took the items out of the cart as well as the twins, setting everything down next to him. Then the platform began to rise.

"Goo ga-a?" Annie asked.

"Oh, yes sorry," the Doctor replied. "This is a planet where the platforms rise - paying platforms are what they're called. They rise so that way someone can't steal any items from the store. The people of this planet may be nice, but they don't want anyone stealing their merchandise."

Annie crawled closer to the Doctor and sat next to his left leg.

The ATM screen flashed a price of all the items that he had unloaded. The platform was not only a way to stop theives, but also to identify the items on the platform. It weighed only the items, and subtrac

ted the weight of the people.

As he paid, he felt that something was a bit off. The shadow was following him again. He could feel it. Annie grabbed his leg and held on, seemingly stronger than the one year old that she really was. The Doctor could hear her sobbing. As he got change back from the machine and the words "Have a Nice Day" appeared on the screen, it finally clicked.

"Arthur!"

Before the platform completely reached the ground, he grabbed Annie and leaped off, looking for the missing baby.

"Arthur! Arthur!" The Doctor knew that even though this was a planet full of people who cared about children, there were still those who could take the baby for evil. Not to mention that shadow- like thing that kept following him. Now it was gone.

Not to mention Arthur wasn't answering. Whatever that thing was, it took Arthur


	2. Chapter 2

Almost seventeen years later...

"ANNIE?"

There was no answer. The Doctor rolled his eyes. When Annie didn't answer, there was only one place she could be in the TARDIS: the swimming pool.

He moved away from the controls and headed down one of the hallways. After making a few lefts and rights, he walked into the swimming pool room. Sure enough, he could see Annie's tanned body moving back and forth in the pool. She looked up from beneath the water and swam upward to meet him at the pool's edge.

"Yes, Daddy?" she asked, taking off her goggles.

"Where'd you put my sonic? I need to fix a few wires under the console."

Annie giggled, telling him, "I needed to use it to fix the door to my room. It kept locking itself. I hope you don't mind."

Of course he didn't mind, but he would have appreciated her asking him. He had told her numerous times to ask him to use his sonic, but she always seemed to be forgetting to do so. If she were a Time Lord, he probably would have gotten her a sonic by now.

"Where is it now?"

"In your room."

The Doctor sighed. He hadn't checked his bedroom. That wasn't the first place he would look. He rarely went in there.

Not to mention he also told her hundreds of times not to put his sonic in his bedroom.

He sighed, "Where in my room?"

"Here, I'll show you."

Annie pulled herself out of the pool, dried off quickly, and wrapped the towel around her body. She slipped on her sandals and walked out of the pool room, her honey brown hair still dripping wet.

She led him to his room, opening the door and heading towards the nightstand from Glifion IV. Annie pressed a few buttons on its exterior and a small drawer opened out and floated in front of them. She pushed the floating drawer towards the Doctor. The Doctor realized that the sonic was in it and using the voice command for the drawer said, "Sonic". Immediately, the sonic floated out of the drawer and into his hand. Then the drawer floated back to the nightstand and slid back in.

"Thank you, Annie."

"No problem Daddy. I think I should go clean my room. I haven't cleaned it since we went to Rasta-Rasta- how do you pronounce it again?"

"Rastaphiloporimapatorp?"

"Yeah. I always get tongue tied pronouncing that one." She said as she went back to her room.

Annie's room was a mess. Then again, she was always too busy travelling through time and space with her dad to really pay attention to the state of her bedroom. When it was clean, it was a very nice room. Light blue walls(blue was her favorite color), cherry wood flooring, beautiful furniture from different planets and several dolls and strange objects that must have been souvenirs from the space travels she'd been on with the Doctor. A laptop lay on a strange looking desk and a Harry Potter book lay next to it.

Annie sighed and looked at the dolls and stuffed animals. She was almost eighteen, she really needed to get rid of those, she hadn't played with them since she was, oh she didn't know anymore, nine or ten?

She went up to the attic to grab a couple of boxes. She met with her father along the way.

"Where are you off to?"

"Just to the attic. I'm putting some old toys up there for storage and am just grabbing some boxes to hold the stuff." she said, walking around her father. "You?"

"Just grabbing some old tools that can do the job the sonic can't."

"Huh. I thought that the sonic screwdriver could fix that console."

"Apparently not all the way, by the way, once I finish fixing the console, shall we do some more travelling?"

Annie grinned. "How about we go to Earth for once, I've never been there." This was true, the Doctor had, for some reason, avoided taking her to her home planet, making it out that she was a humanoid alien like himself, even if she was not Gallifreyan like he was.

"Oh, alright." she had been nagging him about this for at least three years - more - if you counted the year on the planet they were on.

She grinned and hugged him, then walked up to the attic. She gathered a couple of boxes and walked back to her room.

She started with the alien toys, she wrapped each one then placed it carefully in a box she'd labeled with a blue Sharpie and some duct tape she had lying about.

Once she was done with those, she packed up almost all of her old dolls and stuffed animals. She left just one, the well-worn tabby cat she'd named Simon. Her dad had bought it for her when she went to New Earth for the first time when she was eight.

After a little while she'd packed up all the things she wanted to get rid of, or at least put in storage, and took them up to the attic.

She took a quick shower and went down to the control room.

"Daddy?" She yelled.

"Down here!" She heard him say from under the console. She rolled her eyes as she walked down the steps to see her father hanging on a bungee-like thing under the glass floor, practically wrapped in wires as he continued to untangle them and reconnect them by means of a sonic screwdriver and a normal pair of wire cutters.

"Need some help?" she giggled.

"No. I think I've got it. Why don't you go... clean your room some more?"

"I already cleaned it." Sparks crackled, interrupting her. "Ten minutes ago!"

"Oh..." he muttered, still completely focused on the TARDIS and not on her.

She rolled her eyes and went to the wardrobe room to change out of her dressing gown.  
>She found a simple white V-neck T-shirt, black ripped up jeans, pink Doc Martins and headed to the men's jacket section.<p>

She riffled through several coats and jackets, including her dad's spare tweed one and a ridiculously long brown trench coat, before finding a black leather jacket that she liked very much. She slipped it on to find that it fit almost perfectly, just a little long on the arms.

She went back downstairs and found her dad completely tangled up in wires.

"Nice going!" She burst out laughing.

"Oh. Just help me, will you!" She quickly unknotted the wires and offered him her hand.

He took it, pulled himself up,straightened his bow tie, and looked at the jacket. "Where did you get that jacket?"

"In the wardrobe. Why?"

" I wore that in my ninth regeneration." His eyes looked tired and sad, as if a great secret were behind that jacket, or even that regeneration, but then his eyes lit up with a child-like happiness as he said, "It looks great on you!"

"Thanks!" she looked at the console." Finished yet?"

"Just about. Why?"

"Remember? You promised to take me to Earth. And not New Earth. The original Earth."

"Right. It's not all you think. Why do you want to go so bad?"

"I dunno. It's one of the few places we haven't been, I guess." She looked away from him for a moment. "It just sounds so... interesting. I mean, the way you talk about it and all that. Besides, I've never actually seen a full human being before."

He sighed to himself, why didn'the tell her she was full human?

Well it was too late to do that now.

"Shall we go?" She reached for one of the control mechanisms, she was getting freakishly good at steering the TARDIS. She'd been paying more attention than he'd thought.

He only hoped that she would avoid that one place... that one place in particular... anything but Lake Silencio.

When they got out, the Doctor poked his head out. He groaned, it was exactly Lake Silencio.

"Oh Annie, look at the time, we better go!" he said as he started pushing her back in the TARDIS, slamming the door shut behind them. "I just realized that I forgot to show you the dogs with no noses on Barcelona! Much friendlier place anyway!" He started heading towards the console, but Annie still stood at the door, staring back at him.

"Dad, you promised."

The Doctor sighed. "Yes, I know. But we can't go there."

Before she could argue, the Doctor pressed a few buttons and headed towards Barcelona.

They stood there for a few minutes after they landed. Annie didn't move from the door.

"Take me back."

He looked questionably at her. She rarely got mad at him! Usually the only time she got mad at him was when they were in a dangerous place and he didn't want her to step foot out of the TARDIS.

"I only wanted to see Earth. What are you hiding from me?"

"Nothing! Nothing."

She gave him a questionable stare. He avoided it and said, "Fine, we can go back, but we can't go there. We can go anywhere but there. In fact, let's just avoid the United States altogether."

She sighed in relief. "At least we'll still get to go to Earth!"

He pressed a few buttons again and this time they landed in Cardiff.

The Doctor headed her back out of the TARDIS towards a place he'd once fought a wall-walker at. He might as well check Skypoint Apartment Complex to see if it had returned. Annie had not yet forgotten her small argument with her father. She decided she'd figure it out later, as of right now, she was on Earth! She could have jumped for joy.

She watched as the Doctor did several long scans of a building. She looked at the ornate sign outside the front gates. SkyPoint Apartments. She looked up at the building,it was gigantic. At least twenty-five floors high.

She tapped her foot impatiently. "Dad. I wanna see more of Earth than just some gigantic building."

"Just one second..." he took one last scan then stood up. "Alright. Where do you want to go?"

"Anywhere!" She laughed, throwing her hands up and spinning around excitedly. The Doctor rolled his eyes at the young woman's immatureness. She could be quite a young lady. She had almost tricked him once into thinking she was the daughter of a governess. That was how much a young lady she could be. But when she got excited about a new planet... She could be extremely silly and easily excitable.

Of course, he remembered how he was when he first travelled to Earth. He had been so excited to see how such a tiny race of people could always end up surviving. Not to mention their bravery! Although their cities and buildings weren't as extravagant as others, the Doctor was still awed by the human race. Considering that this was Annie's first time on Earth, he could understand her excitement.

Annie looked eagerly around her surroundings. The Doctor trailed along side her, keeping an eye out. For some reason, he felt the same thing he'd felt almost eighteen years ago. On that day. He'd almost forgotten it! And, the boy. He'd forgotten about the boy.

But perhaps it was for the best. The boy had to have been killed. But why would anyone go to such great measures to kill a human boy and leave the girl he was with?

"Dad? Dad. Someone is staring at us." The Doctor came out of his trance.

"What?"

"Someone. Is. Staring. At. Us." She said as she pointed to the dark haired man who was indeed staring at them. Annie made the mistake of making eye contact with the man; he raised his eyebrow in interest, making Annie blush.

The Doctor noticed Annie's reaction and murmured, "Oh no."

Annie broke eye contact with the man and looked at her father. "Is he dangerous?"

"He's probably the most dangerous human in existence," the Doctor stated irritably. But then he added, "He's harmless."

"But you just said-" But then the man walked over to them.

"You'll understand in a few minutes. Come along." He began walking over to the man, Annie following close behind him, a bit puzzled. How was the man dangerous but harmless?

"Hello, Jack." the Doctor said irritably.

The man - Jack - looked surprised. "Hey buddy, I don't know who you are, but..." he paused and grinned at both of them. "I sure don't mind that you two came over here." He turned to Annie. "What's your name?"

The Doctor growled before Annie could answer, "I'm the Doctor, nice to meet you Jack. Now stop flirting with my daughter."

Jack just looked at the man who had called himself the Doctor. "Doctor? Is that really you? You changed...again."

The Doctor cracked a smile. "Yes, well don't get used to me always popping by to say 'hello'."

Jack chuckled, "Don't worry, I won't. So you have a daughter? I always knew that you and Rose would have a kid - "

"Oh no no no no NO!" The Doctor said quickly. "No, she's adopted. I didn't get to tell you: Rose is in the parallel universe with the Metacrisis. It's a long story how I came about Annie."

Annie looked up at the Doctor curiously. 'Who's Rose?"

"Oh - er - no one."

Jack smirked, "Oh come on, did you hide that whole story from her?"

"There is no story, Jack," the Doctor said sternly.

Jack smirked. 'Uh-huh. Sure. Whatever you say."

"There. Is. No. Story!" the Doctor said, the frustration clear in his voice.

Annie put on the stubborn pout she reserved only when she wanted some form of information about someone,something, or somewhere. 'Who is she? Really. My real mum?"

"She's just a former companion Annie."

She gave him a look as Jack smirked again. She turned to him. "Will you tell me who she is?"

"He was in love with her. That's the main thing." The Doctor threw his arms up and shook them with frustration.

Jack rolled his eyes and nodded towards Annie. "What is she?"

"What do you mean?"

"I mean, what type of alien is she? Or is she human?''

The Doctor gulped as Annie looked at him. He had never told her anything about what she really was.

Before the Doctor could answer, a large crash could be heard. The Doctor looked around and Annie immediately handed him the sonic.

"Dad? What was that?" she sounded only partially frightened.

" That is what took your brother, I believe."


	3. Chapter 3

They ran back to the TARDIS. Annie started pacing the console room.

'What do you mean, 'My brother'?"

She, the Doctor, and Jack were panting as they shut the TARDIS doors.

"Well...When I got you, there was a boy called Arthur with you. But I took you two to the planet Bob to pick up some baby supplies and while I was on the paying platform, he was kidnapped.''

"By what?"

"Well, like I said, I think by the thing that made that explosion. But what the creature is...I have no idea."

"So, you've been lying to me."

He sighed. "I'm sorry Annie."

"I know. Just...let me have some time alone to mull it over." She stood up and walked off to her bedroom.

The Doctor buried his face in his hands and sighed.

"That went well." He heard Jack say.

"Not the time, Jack. Not the time." He lifted his face from his hands and stared in the direction of his daughter's bedroom. "Do you reckon she's okay?"

* * *

><p>Annie was not what you would call 'okay'. She was stunned that her father had kept this from her. And for so long! Sure, there hadn't really been a right <em>moment<em> for him to tell her...But still... She sighed and looked around her room.

What else had he hidden from her? Well, there was that incident when he didn't want her to go to that one place when they first landed on Earth. But why had he done that? What was so bad about that place?

Ever since she brought up Earth, her father seemed to be hiding so much from her.

And whole the hell was Rose Tyler? Or this Jack Harkness? Her father usually introduced her to acquaintances, friends, and sometimes even enemies that he had.

But not this time, and it really bothered her.

Annie flopped on her bed, staring at the ceiling. If only she were able to communicate with the TARDIS like her father could. He had told her thousands of times that Time Lords had certain telepathy links with their TARDIS'.

She never thought that she was Gallifreyan. She knew that all the Time Lords were dead except her father. He had told her about the Time War. Of course, he didn't tell her _everything_ about the Time War, only what he thought she needed to know. That was another event that he hid from her. She didn't even know how all the Time Lords died. Was it by an explosion? And if it was, then who caused the explosion? She assumed that it was always the Daleks as they were heading towards their death.

But what if there were some type of third party involved and they did it?

She rolled over on the bed, frustrated. Very little could bother Annie, but there was one thing that could really weaken her senses and her mind: secrets.

Especially secrets that her father had been keeping from her all her life.

Whenever Annie felt like anyone was withholding information from her, she couldn't stop thinking of all the possible things they could be hiding.

Like Rose Tyler. She knew that her father had travelled with other people before. She had heard him throw their names around before. Susan, Sarah Jane Smith, Leela, Romana, Martha, Donna, Rory, Amy - the list went on. But he had never mentioned any Rose Tyler. If Miss Tyler had traveled with her father, then why hadn't her father ever talked about her?

And what had Jack said about this woman? That her father had been in love with this so called 'Rose Tyler'? And then her father had said she was in a parallel universe and is with something called the 'Metacrisis'. And that-what the heck was a 'Metacrisis'? He'd never mentioned that to her. And then there was her brother...Why had he not told her about him? Didn't the sister deserve to know these things?

She rolled over again and stared down at her floor. She knew some stuff. Like how old she was, and that she'd lived with the Doctor her whole life. That much was certain. But what about the other stuff? Which planet did the Doctor find her on? What race was she really from? Who was she? _What_ was she?

* * *

><p>Arthur...The name never really suited him. He was way too powerful to be a mere 'Arthur'. In Earth legends, "Arthur" was a name of a king who fought for the good of his country. This king believed in the equality of his "knights" and had them sit at a round table so that not one of them would think he was greater.<p>

However, Arthur, the one sitting in the chair at the ship's console, felt nothing like this king.

He had power. Oh yes, he had power to boot. But he was not the loyal and trustworthy king that the legendary King Arthur of Earth was. And yet, he didn't mind.

So instead, his crew knew him as "Captain" and nothing else.

"Captain, we have arrived at our destination."

"Thank you, Lieutenant," he said dryly as he stood up. "I'll be in my cabin. Prepare the crew for disembarkment."

He stalked down the hallways quickly and silently as if he were a phantom, heading towards his cabin. He hated Earth. The people who inhabited it were ignorant and weak. They assumed that they were the only beings in the universe - ha!

The door to his cabin slid open as he approached and closing behind him as he entered. Unlike the rest of the ship, the room was not all that dark. Actually, it was a light navy blue.

He headed towards the mirror; he had to make sure that it would still stay in place - his eyepatch that is.

He remembered full well how he had gotten this eyepatch. There were lasers firing everywhere on the battlefield. He had seen dozens of his comrades fall at the mercy of the enemy. But he wasn't about to let this one go.

The soldier had been loyal to him and their cause since the very beginning. He had been raised by it, but this one had been taken in. They had fought side by side hundreds of times before. Hundreds had fallen at their feet. Many had tried to rebel. But they had never even considered that. They needed the power that was offered to them. But more than that, they needed each other.

And now she had been shot. Arthur knew that she was a human, and that her wound was fatal, but maybe, just maybe, he could get her to safety. He could probably get her back to the ship. The communicator had fallen from his belt hours before, so there was no way he could get help at that moment. He was only searching for a temporary place of shelter for her until he could find another communicator to ask for help.

Climbing a dirt mound, Arthur began gasping heavily. He was wounded as well, his side had been shot. But he couldn't afford to rest even for a second. He had to get her to safety.

To his horror, something else met him at the top of the mound. Its metal exterior gleamed in the moons' light and its bright green eyes glared at him in hatred.

"You're trying to kill us," it stated.

Arthur didn't know how to respond. All he could think about was getting her to safety. He looked at it right in the eye and begged, "Please."

Looking at it in the eye was a mistake. These creatures had a defense mechanism when looked at in the eye. Arthur had momentarily forgot it in his despair and hopelessness.

Memory returned to him and he sharply turned his head to the left. A dark green laser shot out of the creature's eyes, hitting Arthur's right eye as well as his right cheek.

Arthur's eye stung at the memory, and he rubbed it irritably. Now all that was left was an empty socket and a long scar on his right cheek and forehead. His comrades had done their best to repair him, but this was the best he could do.

And he couldn't afford a new eye.

"Captain," a voice said on the intercom. "We're ready for you."

He sighed, straightened his black and blue uniform, and grabbed his black cloak as he headed through the door. He put it on as he gingerly walked through the hallway.

He smirked as he looked out the windows of the unloading dock.

"Earth almost looks... beautiful, at this time of year." He chuckled. "But it might look even better when it's all turned to dust."

* * *

><p>Annie was still frustrated. She couldn't figure any of it out. Like, why had her dad kept this from her? What else had he kept from her? Knock, knock, knock. She heard a gentle rapping on her door.<p>

"Come in." She was expecting her father, but instead it was that strange Jack Harkness. "Oh, it's you. What do you want?"

"Your father needs to tell you something. And I just wanted to see you." He smirked.

She growled. "This is one of the reasons I'm not into men like you."

She got up and walked out into the control room, grumbling about overly flirty guys. She'd never liked them. Let alone_ trust_ them! She'd always liked calmer, more sophisticated, less flirty males. Then again, they were a whole other species to her.

When she got to the control room, she found her father sipping a cup of tea. "What is it Dad?"

He sighed. "Look Annie, there's something else I've been meaning to tell you for a long time. In answer to Jack's former question."

"Which one?" Jack had entered the control room.

"The one where you asked what species she was."

"Oh!" Jack walked over to them.

Annie looked intently at him. "Well? What am I?"

"You're-uhm." He tried to stall. It had been a very long time since he and his daughter had had a fight. On Earth, he supposed she was a 'Daddy's Little Princess'.

"I'm a what, Dad?" She wasn't going to let up. She had waited all her life to find this out. She knew she was some kind of alien, she just didn't know which kind exactly.

'Well-er-you're a..."

"Will you stop stalling and just TELL me? !"

"Well...You're human, Annie."


	4. Chapter 4

**Chapter Four**

"Excuse me?"

"You're human."

"But-" she started laughing. "Ha-ha. Very funny. Alright, really, what am I?"

"Human."

"You're serious?"

He sighed. "I don't know why I-" But she had left the room.

Annie paced about her bedroom. She was more surprised than angry though. _'Why did he keep this from me? I thought he would tell me everything_!' she thought.

She groaned and pulled a book from her bookshelf. She tried to read it, it had been one of her favorites as a little girl. Her father had read from it to her every night. She had two copies. One in English, so she could read it easily, and one in its actual language, which her father was still teaching her. It was a book of fairy tales from her father's planet.

She tried to read from it, but her frustration pounded inside her skull and prevented her from being able to read the book. She threw it aside, managing to knock over her laptop.

She sighed with frustration and set it right again. Maybe a little fresh air would clear her mind? She pulled open the door to her bedroom, snuck through the console room, pulled open the door, and went outside.

* * *

><p>Sitting down beside the TARDIS, she closed her eyes. The outside world was a calming place to her. It always had been after an argument with her father, even though that rarely happened. She breathed in the air that was so new, yet in a way, familiar. Opening her eyes, she looked up at the night sky. They were the same stars that she had seen her whole life, whether she had traveled to them or seen them in other night skies on other planets or stars. But this view... it was unbelievable.<p>

She stood up. She needed a walk.

As she started walking, she became vaguely aware of a funny feeling. She felt as though someone was following her, or near her in any case. All she knew was that she could definitely not be alone wherever she was. But who was there? She whipped around, but saw no one. She walked quicker and heard a leaf crunch behind her. She turned again. No one.

* * *

><p>Jack had returned to Torchwood hours ago. Now the Doctor was alone in the TARDIS.<p>

The Doctor had been in his room for a while, thinking about Annie. She had always seemed fascinated with humans, just like he was. He couldn't blame her; he always spoke of them as if they were universe-changers. But they were. In such small ways, humans could change the course of time, even though they were such a small species. He had always been one for underdogs.

But there were also so many things wrong with humans. Oh! The Doctor could fill books telling of all of mankind's weaknesses! He had tried to explain that to Annie years ago when she had asked him about it, but she still didn't quite understand. He supposed she had to learn the hard way.

However, she didn't have to.

He got up and walked to Annie's room. Hesitantly, he stood at the door.

"Annie?" No answer.

He sighed, "Annie, I know this might be very hard for you to understand right now." Still, no one replied. He continued, "Listen, I think that maybe we should come to Earth some other time. It might not be very good to come here right now. Maybe we could go to Barcelona... Annie?"

He jiggled the handle a bit, and although it was supposed to be locked, the door creaked open.

"Annie?"

He opened the door wider and looked into the room. Not a soul was in that room.

The Doctor rushed to the pool room sure his daughter had gone swimming to clear her mind, but the water was still. In the library, none of the books had been touched. In the game room, all was silent.

He ran outside, to the fresh clean air of Earth. Then he made the mistake of looking ahead.

* * *

><p>Arthur hadn't been to Earth in quite a while. He had been there when he was very young, maybe when he was about four years old. The air was much different than that of other planets, and its cool breeze almost made him delirious. He had separated from the rest of his crew twenty minutes ago, all of them scouting out the area.<p>

Now he was on an empty street. He crept along it silently. Passing an old blue telephone box and turning left, he saw a girl walking with her shoulders slumped. Her black leather jacket was a bit long on her and her long honey brown hair was slightly damp, as if she'd taken a shower a while ago.

He made his way over to her, smirking. Maybe she could help him.

* * *

><p>"Hey," Annie heard a soft voice behind her. Even with that one word, Annie could hear its seductive purr.<p>

She didn't turn around, saying stiffly, "Hello."

"Oh, don't be like that. I'm not so bad." A pause. "Besides, you seem like a really nice girl."

Annie growled, "Leave me alone."

The man behind her sighed. "Look, I know it's been hard for you. And you probably have a lot on your mind... but I want you to be happy."

"What are you talking about? I'm fine." Annie sat down on the sidewalk.

The man sat down next to her, but she didn't look at him.

"Hey, you could always stay with me for a while. I might need help."

She sighed and looked at the man right in the eye. "Look, Mr. Harkness -"

"Mr. Harkness? Oh c'mon. You can call me Jack."

"Okay then, Jack, you know that I can't do that. It'd just break his hearts..."

Jack touched her hand. "I'm not talking about forever, sweet Annie. I'm just saying you can stay with me awhile so both of you can blow off some steam. Trust me, I know." He sighed. "It's what always worked for me."

"I don't know, Jack..."

"Annie?"

She looked at Jack. "Yeah?"

"I really do think it will help."

The way his voice sounded was so soft and so welcoming. Annie could feel herself drawing nearer to the man that she thought she despised.

"And you can stay here in Cardiff for a while at Torchwood. We help save the earth... kind of a lot. You'd be right at home."

Annie giggled and unconsciously moved closer to him. Jack smiled, hoping that he could help comfort her. If all went well, then both she and her father would be happy just like they had been before.

But the Doctor could be so unpredictable...

"But would that be alright?" Annie asked.

"Hm?"

"Would it be alright if I stayed at Torchwood for a while."

Jack cracked a smile. "Oh I'm sure the team wouldn't mind. They'd love to have you around."

Annie's eyes sparkled, but she shivered at the cold. Jack wrapped her in his arms and she snuggled into his arms. They sat like that for a few minutes until Annie looked up at him again. He didn't seem to be such a bad person after all...

"Annie..?"

"Hm...?" She was lost in his eyes.

He leaned in towards her and kissed her. And Annie kissed back.

* * *

><p>The Doctor watched in horror. Then finding his voice again, he shouted, "Jack, get off of my daughter!"<p>

Annie and Jack quickly pulled away from each other, the moonlight showing that both were now blushing.

"Dad! I-"

"What. Were. you._ THINKING_? !"

"That if i stay with you, I'd never experience the things_ humans_ and even _aliens_ get to experience! A _kiss_!"

"You've kissed me hundreds of times."

"In a daughterly way! Not, like, _THIS_," Annie was obviously close to tears. She'd always gotten upset easily.

"Is that what you want? To lead a normal life?" The Doctor said this as if it were venom in his mouth

Annie picked up on this, "What's wrong with a normal life? What's wrong with being human? After all, _you said_ that I'm human. Maybe it's about time I started acting like one!"

He himself was close to tears. He had to fix this. But he didn't know how.

"Whoa. You two calm down."

"Shut up Jack. How dare you try to seduce her?"

"Doctor. Leave him alone."

The Doctor almost gasped. Annie had _never_ before to his knowledge called him 'Doctor'. It was always 'dad' when she was teasing, 'daddy' was the most common, and 'father' when she was irritated. But _never_ '_Doctor'_!

"Annie. I...I'm..."

"First you keep secrets about Earth, then about Jack and Rose Tyler, whoever she is, then about my being human. Why should I believe you anymore Doctor?"

"Stop calling me that! To you,I'm daddy, aren't I?"

"Why should you be?"

Oh no. Not that. Anything but her saying he was not her father.

"Jack offered me a place at Torchwood. Maybe I _should_ take it."

"_NO_!"

Annie huffed, "Well what do you expect me to do, Doctor? After all that's happened, do you just expect me to just go on travelling like nothing ever happened?"

The Doctor sighed and remembered all the danger he had ever put her through. He didn't want her to go through all that pain again. Or even face worse than before.

He looked over at Jack, who was trying to hide his awkwardness by giving the Doctor a weak smile. The Doctor looked back at Annie, once again looking composed. Fine, he had torn his hearts out of his chest and broken them into little pieces. And she had kissed Jack Harkness out of all the men that she could have kissed. But he still knew what was best for her.

Which is why he did the unexpected.

"Alright, Annie," he began. "I'll let you live on Earth."

Annie's eyes widened and her expression showed confusion. "What?"

"You can stay here on Earth."

Annie's anger subsided. She looked at her father, then back at Jack Harkness. She remembered the type of man that Jack was. What was she thinking? She couldn't stay at Torchwood with that man. Deep down, she knew that he didn't love her, or at least not the way she would want him to.

"No, I want to stay here," she said with a distant voice, looking at the Doctor. But he returned her expression with one that she had only seen him give to only a few others. He looked at her as though she were separate from him and that she was just another alien to him.

Her face paled. She knew what he did to those he gave that expression to.

"Daddy, I'm sorry..."

The part that terrified her was the lack of expression he had. It was as if he were a statue. Or maybe a weeping angel. She was waiting for him to have that ugly expression once she blinked. She blinked. Nothing happened. His expression stayed the same.

"Annie, you don't understand. You never understood anything about me."

She was confused again, but didn't need to ask him to clarify it.

"You never understood what I had to do to protect you. You can't possibly understand why I had to keep everything from you. You're only _human_." He looked her in the eyes, but was still able to ignore the pleading that was so evident in them.

"I should never have taken you in. All I ever did was ruin your life."

"No! Daddy -"

"No, you need to live a human life. After all, that is what you _really_ want. Then go ahead. _Leave_."

Jack stepped in. "Doctor, it really was my fault, don't do this to her."

The Doctor glared at Harkness. "This is for her own good. It had to happen sooner or later. Take her in. All she knows is the universe. Maybe you can still show her some of it."

All Jack could do was nod. He walked over to Annie. "C'mon, sweet Annie."

He gently tugged her arm.

"_No_!" She nearly screamed. The Doctor gave her a long look as though he was observing her. She tried looking into his eyes, but just like the rest of him, they were cold.

"_Daddy_..."

There was a tug at her arm again. "C'mon."

"No..."

The Doctor turned away from her and went back to his console.

Annie turned away and walked out the door with Jack,tears pouring down her cheeks. But she looked back for just one moment before the door closed. And in that moment, she could have sworn that she had seen her father look back at her, with a tear sliding down his cheek.


	5. Chapter 5

It had been a, well, there really wasn't any other way to put it, a _boring_, day at Torchwood, at least... it was boring so far. No aliens, no saving the Earth, hell, not even a Weevil attack! Just piles and piles of reports to sort through, computers to work on, and alien instruments to test. A dull day at work.

Mind blowingly bored, Annie took off into the cold winter that was blowing outside the Hub.

She took a long stroll through the city before realizing how cold she was. She took a quick look at her surroundings to judge how far she was from the Torchwood base. Recognizing the small shopping area, she calculated that she was about ten miles away from Torchwood.

She shivered and realized that her hands had gone numb with cold. She checked her watch, it was ten minutes until noon. She shrugged, she had time for a cup of tea and a sandwich before heading back. She turned around and headed into the small cafe around the corner. She pulled open the door and saw that there really was only one or two other people in the cafe, most of Cardiff were staying inside these days, avoiding the cold weather.

She sat down at a booth and picked up the menu. She had just decided on a cup of raspberry and honey tea (her favorite) and half a ham sandwich when a voice spoke up.

"You look like you need someone to talk too."

She looked up to see a red haired boy about her age in a waiter's uniform looking at her. '' That would be nice." She said, smiling.

He sat down across from her. "I'm Eli by the way. Eli Crewe."

She smiled and stuck her hand out. "Annie. Annie..." she paused, deciding what her last name should be before deciding on her dad's fake last name. "Smith."

"Nice to meetcha! Now, what's wrong?"

"Just... work problems."

"Ah. Hard ass boss?"

"No. It's just, I can't do what I really want to do at work."

"Ah. Neither can I. I'm working part time here to pay for college. You?"

"Yeah. Same."

He smiled. "Where do ya work?"

"Can't really explain. It's still a working progress."

"Ah. You could get a job here. We could talk more." He grinned at her, making Annie go scarlet.

"We could, couldn't we." She said, grinning back in the same manner that Eli was.

* * *

><p><em>Six months later...<em>

"Who is he Annie?" Jack suddenly asked, as he watched Annie put an almost nude colored pink lipgloss on her lips. Something she only did on occasion, for an important event.

"I have no idea what your talking about." Annie said, flicking on mascara now.

"Don't lie. I've been noticing you wear more makeup, dressing even nicer than usual, going out more, even in the winter. Come on. Who is he?"

She blushed. "Alright. Alright. His name is Eli Crewe. We met at the cafe down the road. He's super nice and really funny."

"How long?"

"Not long. We've been friends for six months. This is honestly our first 'date'."

'Nice! Congratulations. Hope it works out well." he said, making Annie go even darker red in the face.

"Yeah. me too."

'Where's he taking you?'

"To an old fashioned sci-fi movie fest."

"He picked something just right for you. Does he know, about us?"

"No. I haven't told him about Torchwood."

"Good. First make sure he's definately the one."

"M'kay." she dabbed a bit of her faintest perfume on her wrists and her neck and stod up. "How do I look?"

Annie was dressed in an almost sailor dress. It was navy blue with white lining and a set of large white buttons on either side. She looked quite ute.

"Very pretty. Now go!" Giggling at the way he was acting like an uncle, at least, how she _thought _an uncle would act seeing as she never had one in the first place, she left the Hub and met up with Eli at the corner.

"You look really pretty Annie." he said as she giggled under her breath.

"Thanks El." she said, using her personel nickname for him.

"No problem. Now come on! That movie fest will start whether or not we're there!" he offered her his hand, she took it, and the two ran to his car.

Annie looked at him. The dark red hair had become a bit shaggy over the last six months, his dark eyes twinkled and she couldn't help but smile. She had been attracted to many men, mostly celebrity crushes, but the day she had met Eli, she realized that he had pretty much stolen half her heart and had stored it away for safe keeping.

She had lost interest in aliens, in Torchwood, even in searching the sky for the TARDIS. In fact, she had gone and done the most human thing she could possibly do. She had fallen in love. And the thought terrified her.


	6. Chapter 6

**NOTICE:**

Dear fans of Secrets. I've very sorry to tell you this but the story '_Secrets'_ has been cancelled on this account due to one of the writer's always being busy. _**BUT**_the story of Annie does not hang of a cliff. I am prepared to take on the task myself. If you are interested in continuing the story of Eleven's adopted daughter, go to the account _Torchwooder98_. And you will find it.

Torchwooder98.


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